I would need to see some code or some of the files from the tars to make any informed guesses.

Without any other evidence, I'd say it's probably a LF vs CRLF thing.

"WE ARE speaking of a plague that consumes an estimated $75 billion per year of public money, exacts an estimated $70 billion a year from consumers, is responsible for nearly 50 per cent of the million Americans who are today in jail, occupies an estimated 50 per cent of the trial time of our judiciary, and takes the time of 400,000 policemen -- yet a plague for which no cure is at hand, nor in prospect."-William F. Buckley, Jr. 1996